Our Science

Overview

Aging is a growing problem for both individual quality of life and the economics of societal health. Age is the primary risk factor for the majority of the top causes of death in the United States. My laboratory uses systems and comparative genetics to identify and characterize novel mechanisms of aging. By understanding the molecular architecture that drives aging, our goal is to identify key intervention points to simultaneously delay onset of many age-associated diseases and extend healthy lifespan. We employ a formal experimental pipeline that leverages the strengths of four model systems—humans, cell culture, mice, and nematodes—to (1) generate candidate interventions or intervention targets through systems-level studies in humans, (2) screen candidate interventions for extension of lifespan or other age-related phenotypes in the nematode Caenorhabditis elegans, (3) characterize mechanisms of lifespan extension for selected candidates in C. elegans, (4) validate mechanistic models and examine tissue-specific phenotypes in mice and cell culture, (5) develop targeted interventions to slow aging or treat age-associated disease in mice, and (6) translate promising interventions to the clinic. Through application of this pipeline, we have developed a molecular focus on understanding the complex interaction between metabolism and stress response during aging. We also support this pipeline through the development of new tools for high-content aging analysis in C. elegans. The sections below highlight ongoing projects in the Sutphin Lab.

Targeting kynurenine metabolism in aging

The kynurenine pathway—the major metabolic route for ingested tryptophan—becomes dysregulated with age and is implicated as a driver of aging. We find that elevating physiological levels of the kynurenine pathway metabolite 3-hydroxyanthranilic acid (3HAA) through dietary supplementation or inhibition of 3HAA dioxygenase (HAAO) extends lifespan and metrics of late-life health in both C. elegans and mice. Understanding the mechanisms that mediate the benefits of 3HAA and developing 3HAA-based therapeutics for aging is a major focus of our research. Current projects are focused on optimizing 3HAA for lifespan extension and impact on immune function and stress resilience.

  • Elevating 3HAA through either 3HAA supplementation or HAAO inhibition robustly extends lifespan in C. elegans and produces sex-specific lifespan extension in mice. We are working to understand the mechanisms underlying these benefits and to develop pharmacological strategies to elevate 3HAA.

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  • We find that C. elegans with elevated 3HAA are resistant to multiple forms of exogenous stress, including both protein misfolding stress and oxidative stress. Ongoing work is focused on understanding the underlying mechanisms and determining whether the same is true in mammals.

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  • We find that C. elegans with elevated 3HAA are resistant to bacterial pathogens. 3HAA has direct antimicrobial activity and co-localizes with engulfed bacteria in C. elegans gut granules. In ongoing work we are dissecting the molecular mechanisms that mediate these observations in C. elegans. We are also testing the hypothesis that 3HAA will reduce chronic inflammation and improve aging immune function in mice.

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Defining the genetic architecture of multiple stress response

The goal of this work is to understand the fundamental biology of cellular response to different forms and combinations of stress. Cells are constantly subjected to intrinsic and extrinsic stresses—reactive oxygen species, protein misfolding, osmotic stress—that negatively impact cellular structure and function. In response, cells activate a range of molecular pathways to mitigate and repair damage—oxidative stress response, unfolded protein response, osmotic stress response. Several interventions that improve health, such as dietary restriction, both activate stress response pathways and promote multi-stress resistance. While individual stress response pathways are reasonably well defined, how stress responses differ when cells are challenged with multiple forms of stress simultaneously is less well understood and represents a critical knowledge gap. This gap has broad implications for medicine. Human diseases rarely involve a single form of stress—Alzheimer’s disease is characterized by neuroinflammation, increased oxidative stress, and accumulation of misfolded proteins, while cancer exhibits oxidative stress, DNA damage, and localized hypoxia. By understanding the network of molecular pathways that define cellular stress response, we aim to identify intervention points that can be targeted to activate distinct stress response profiles that improve health, combat disease, and enhance resilience. The long-term goal of this research program is to answer fundamental questions about the biology of stress response: (1) How is the molecular stress response network organized? (2) Which elements of this network are general (responsive to many types of stress) and which are specific (responsive to specific stressors)? (3) How does the cellular response to one type of stress alter an organism’s resistance to other types? (4) Are there key molecular nodes in the stress response network that can be targeted to improve health or treat specific diseases?

  • This project specifically looks at copper and its protective effects against multiple other forms of stress in C. elegans. While Cu is toxic to worms, we find that it also imparts resistant to many other stressors, including osmotic protein misfolding, and Golgi stress. Previous work attributes Cu toxicity to ROS production via a Fenton-like reaction or protein misfolding. Surprisingly, we find no evidence that Cu promotes ROS generation, protein aggregation, or activation of the oxidative stress or unfolded protein response in C. elegans. This suggests that Cu toxicity and stress response in C. elegans work through a previously undescribed mechanism. Cu does modulated bacterial immune pathway and Cu-induced resistance to pathogenic E. coli requires the immune responsive pmk-1 pathway. Cu also remodels expression genes that regulate transport and storage of Fe and Zn. Recent evidence suggests that Cu and Zn are co-regulated and produce synergistic toxicity in C. elegans. The goal of this research is to identify key intervention targets in the copper-response pathway that will have wide-ranging benefits across many categories of health and disease. Ongoing work aims to identify stress pathway mechanisms that can be exploited for use in treatment of illnesses related to chronic environmental stress.

  • This project is focused on understanding the role iron and zinc in aging and cellular stress response. Iron and zinc are both essential elements required for many processes involved in critical life functions. iron is involved in the production of hemoglobin and myoglobin, acts as an enzyme cofactors, and is essential for cellular metabolism. Zinc plays critical roles in immune function, cellular metabolism, and DNA and protein synthesis. Dysregulation and disruption of these processes are known contributing factors to aging. Both elements are tightly regulated and imbalances can contribute to a variety of diseases including cardiovascular disease, Alzheimer's disease, and cancer. Over abundance of both iron and zinc can lead to disruption of many cellular processes and impose stress upon cells through the generation of free radicals. We find that the cellular iron and zinc homeostasis are implicated as mediators of the benefits of kynurenine pathway interventions in both aging and immune function, in the response to many forms of stress, and in host-bacteria interactions. The goal of this project is to dissect the role of iron and zinc homeostasis in aging and cellular stress response.

  • This project focuses on Forkhead Box O (FOXO) transcription factors role in differential stress resistance in breast cancer. Specifically, I am looking at how distinct patterns of FOXO nuclear localization and activation influence cell survival or death. By understanding the mechanistic differences between the response of normal and cancer cells to fasting, our long-term goal is to develop targeted therapies that selectively sensitize cancer cells to chemotherapy while protecting normal cells.

  • The importance of intestinal bacteria in host stress response is an emerging topic of interest. Modulation of innate immune pathways is a shared response to many forms of stress, while the type and stress resistance of the bacteria fed to C. elegans strongly influences host stress resistance. Here we will examine the mechanisms mediating the interplay between host and bacterial stress response. We are particularly interested in understanding role of metal homeostasis in the impact of bacterial stress response on host health. We aim to answer several key questions: Does elevated intestinal bacteria stress resistance broadly confer stress resistance to the host animal? What mechanisms govern bacteria-mediated host stress resistance? Do changes in host and bacterial metal homeostasis mediate coordinated stress resistance?

Technology development for high-content aging research

A major focus of our laboratory is the development of new technologies and methods to accelerate aging research. We are particularly interested in advancing tools for high-content screening in C. elegans. Recent technological advances bring us to the cusp of true high-content data collection methods for long-term tracking of individual Caenorhabditis elegans. C. elegans is a major experimental system across many disciplines ranging from the fundamentals of molecular and cellular biology to complex multicellular processes like development, aging, stress response, neurobiology, and behavior. C. elegans’ popularity reflects its many attractive experimental features—ease of maintenance, rapid reproductive and life cycles, a well-characterized genome, and the availability of a wealth of powerful molecular tools. Standard methods typically examine group-cultured animals on solid media or, more recently, individually cultured animals in microfluidic devices. The former is amenable to high-throughput applications but is usually restricted to one or a few phenotypes per group. The latter provides single-animal resolution, which is important for understanding individual variation in a process of interest and the underlying interaction between molecular drivers of that process, but is difficult to scale and involves culturing animals in liquid media, which induces distinct physiological responses relative to standard growth on solid media. There is a growing critical need for tools that allow high-throughput collection of high-content data in individual animals throughout life. The foundation for building these tools is established by recent advances in solid media-based single-worm culture systems, automated data collection for physiological phenotypes like survival and activity, and automated quantification of fluorescent biomarkers. Over the past several years we have developed a culture system and a robotic imaging platform (Nemadex) that enables automated measurement of multiple physiological characteristics—survival, activity, health—longitudinally in isolated individual C. elegans. In parallel, we have developed analytical tools for rapid, autonomous quantification of fluorescent biomarkers reporting activity in a wide range of molecular processes. In building Nemadex, we have developed a number of focused tools for single-worm culture, rapid fluorescence quantification, and tracking of bacterial colonies in the C. elegans intestine.

  • Nemadex is our robotic imaging platform that enables high-content data collection in C. elegans. Each Nemadex platform can monitor ~19,440 animals in parallel (~150,000 animals per year) cultured on WorMotel single-worm culture environments. Nemadex is also compatible with other culture methods. At present, Nemadex can capture lifespan, healthspan, and daily activity. We are now in the process of incorporating daily multi-channel fluorescence imaging, which will enable flexible lifelong tracking of molecular biomarkers.

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  • Worm Paparazzi is the image processing and analysis pipeline that converts raw images collected on Nemadex into processed lifespan, healthspan, and activity data.

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  • LightSaver is a data analysis package designed to rapidly extract quantitative fluorescence data from C. elegans images.

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  • The most common approach for conducting aging studies in C. elegans, including survival analysis, involves culturing populations of tens to hundreds of animals together on solid nematode growth media (NGM) in Petri plates. While this approach gathers data on a population of animals, most protocols do not track individual animals over time. We have optimized two single-worm culture systems, the WorMotel (originally developed by Chris Fang-Yen's laboratory) and a Terasaki tray-based system (developed by us), that allow longitudinal tracking of individual animals over the course of their lifespan. These culture systems are compatible with both Nemadex and with fluorescence imaging.

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    • Gardea et al. (2022) JoVE [PubMed]

    • Espejo et al. (2022) JoVE [PubMed]

  • Caenorhabditis elegans are an important model system for host-microbe research due to the ability to rapidly quantify the influence of microbial exposure on whole-organism survival and rapidly quantify microbial load. To date, the majority of host-microbe interaction studies rely on host group survival and cross-sectional examination of infection severity. We developed a new system called Systematic Imaging of Caenorhabditis Killing Organisms (SICKO) capable of characterizing longitudinal interactions between host and microbes in individual C. elegans, enabling researchers to capture dynamic changes in gut colonization between individuals and quantify the impact of bacterial colonization events on host survival. SICKO provides a powerful tool into understanding underlying mechanisms of host-microbe interaction, opening a wide avenue for detailed research into therapies that combat pathogen induced illness, the benefits imparted by probiotic bacteria, and understanding the role of the microbiome in host health.

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    • Espejo et al. (2023) bioRxiv [bioRxiv]

Cholesterol metabolism in aging and age-associated disease

Cholesterol has long been a boogeyman in human health, with good reason. Circulating cholesterol is associated with increased risk for multiple diseases of aging, particularly cardiovascular disease. However, this risk comes not from cholesterol itself, but the low-density lipoprotein (LDL) particles that transport cholesterol from liver to peripheral tissue. Most cholesterol is not in circulation but localized within our cells, where it plays vital roles in membrane structure and the production of hormones, vitamins, and bile acids. We recently discovered that cholesterol supplementation robustly and dramatically extends healthy lifespan in the roundworm C. elegans. Our objective in this project is to identify the genes and molecular processes downstream of cholesterol that mediate these benefits. Our long-term goal is to target these processes directly, capturing the benefits of cholesterol without increasing LDL. Indeed, we aim to combine our targeted approach with LDL-lowering therapies to achieve synergistic benefit in the context of healthy longevity.

  • Traditionally viewed as a boogeyman in human health, higher cholesterol diets have been shown to extend lifespan in multiple model organisms. One major focus of this project is on using molecular/genetic tools and imaging techniques to understand the biological consequences of a high cholesterol diet in C. elegans, what molecular processes mediate the observed health benefits, and how these biological consequences promote healthy aging.

  • Our bodies tightly regulate cholesterol production and localization between tissues, and across membranes within individual cells. Cholesterol is transported between cells and tissues, and between organelles with cells, by a complex regulatory system. One of our major goals is to understand which cholesterol transport machinery is important for the health benefits of cholesterol supplementation in C. elegans.

  • Unexpectedly, we observe the lifespan benefits of cholesterol in terms of C. elegans longevity and healthspan when worms are cultured on WorMotel single-worm culture environments but not on standard Petri plate environments. This suggests that the benefits of cholesterol are dependent on the environmental context. In ongoing work, we seek to understand the molecular processes that mediate the observed interaction between supplementary cholesterol and the C. elegans environment.